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- PDB-4j6x: Crystal structure of Hfq from Pseudomonas aeruginosa in complex w... -

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Basic information

Entry
Database: PDB / ID: 4j6x
TitleCrystal structure of Hfq from Pseudomonas aeruginosa in complex with UTP
ComponentsProtein hfq
KeywordsRNA BINDING PROTEIN / LSM / RNA chaperone / sRNA / mRNA
Function / homology
Function and homology information


regulation of carbon utilization / regulation of translation, ncRNA-mediated / regulation of RNA stability / quorum sensing / regulation of translation / regulation of DNA-templated transcription / RNA binding / cytosol
Similarity search - Function
RNA-binding protein Hfq / Hfq protein / SH3 type barrels. - #100 / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / RNA-binding protein Hfq
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.222 Å
AuthorsNikulin, A.D. / Murina, V. / Lekontseva, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Hfq binds ribonucleotides in three different RNA-binding sites.
Authors: Murina, V. / Lekontseva, N. / Nikulin, A.
History
DepositionFeb 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein hfq
B: Protein hfq
C: Protein hfq
D: Protein hfq
E: Protein hfq
F: Protein hfq
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,59212
Polymers54,6876
Non-polymers2,9056
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11450 Å2
ΔGint-87 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.580, 73.520, 107.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Protein hfq


Mass: 9114.487 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: hfq, PA4944 / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HUM0
#2: Chemical
ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 200 mm ammonium sulphate, 200 mm NaCl, 50 mm TRIS-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 22, 2012 / Details: helios
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→25 Å / Num. all: 24556 / Num. obs: 24556 / % possible obs: 99.18 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 13.12
Reflection shellResolution: 2.22→2.34 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 3.12 / Num. unique all: 3419 / % possible all: 94.01

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHENIX(phenix.refine: 1.8.1_1168)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
PROTEUM PLUSPLUSdata reduction
SCALAdata scaling
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U1S

1u1s


Resolution: 2.222→25 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2566 1244 5.07 %random, 5%
Rwork0.1827 ---
all0.1864 24555 --
obs0.1864 24555 99.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.222→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3229 0 174 290 3693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073481
X-RAY DIFFRACTIONf_angle_d1.2994761
X-RAY DIFFRACTIONf_dihedral_angle_d22.0831351
X-RAY DIFFRACTIONf_chiral_restr0.085561
X-RAY DIFFRACTIONf_plane_restr0.005567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.222-2.31090.35881340.28382420X-RAY DIFFRACTION95
2.3109-2.4160.321460.24612527X-RAY DIFFRACTION99
2.416-2.54320.27981320.22632576X-RAY DIFFRACTION100
2.5432-2.70240.28071300.2112581X-RAY DIFFRACTION100
2.7024-2.91070.29951570.20572574X-RAY DIFFRACTION100
2.9107-3.2030.26451310.18072620X-RAY DIFFRACTION100
3.203-3.6650.24961350.1612606X-RAY DIFFRACTION100
3.665-4.61210.2111400.13212638X-RAY DIFFRACTION100
4.6121-23.89820.2121390.16652769X-RAY DIFFRACTION100

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